csaw
This is the released version of csaw; for the devel version, see csaw.
ChIP-Seq Analysis with Windows
Bioconductor version: Release (3.22)
Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
Author: Aaron Lun [aut, cre], Gordon Smyth [aut]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
Citation (from within R, enter
citation("csaw")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("csaw")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("csaw") Reference Manual
PDF
NEWS
Text
Details
biocViews
Annotation, ChIPSeq, Coverage, DifferentialPeakCalling, Genetics, MultipleComparison, Normalization, Sequencing, Software
Version
1.44.0
In Bioconductor since
BioC 3.0 (R-3.1) (11 years)
License
GPL-3
Depends
R (>= 3.5.0), GenomicRanges(>= 1.61.1), SummarizedExperiment(>= 1.39.1)
Imports
Rcpp, Matrix, BiocGenerics, Rsamtools, edgeR, limma, methods, S4Vectors, IRanges, Seqinfo, stats, BiocParallel, metapod, utils
System Requirements
C++11, GNU make
See More
Suggests
AnnotationDbi, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat, GenomicFeatures, GenomicAlignments, knitr, BiocStyle, rmarkdown, BiocManager
Enhances
Depends On Me
csawBook
Links To Me
Build Report
Build Report
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package
csaw_1.44.0.tar.gz
Windows Binary (x86_64)
csaw_1.43.1.zip
macOS Binary (x86_64)
csaw_1.44.0.tgz
macOS Binary (arm64)
csaw_1.44.0.tgz
Source Repository
git clone https://git.bioconductor.org/packages/csaw
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/csaw
Bioc Package Browser
https://code.bioconductor.org/browse/csaw/
Package Short Url
https://bioconductor.org/packages/csaw/
Package Downloads Report
Download Stats